-------------------------------------------

To detect which indexes are not used.
ref: https://www.databasejournal.com/mysql/an-overview-of-the-mysql-performance-schema/

SELECT object_schema, object_name, index_name
 FROM performance_schema.table_io_waits_summary_by_index_usage
 WHERE index_name IS NOT NULL
 AND count_star = 0
 ORDER BY object_schema, object_name;

Also, finding hogging queries

SELECT PROCESSLIST_ID AS id, 
        PROCESSLIST_USER AS user, 
        PROCESSLIST_HOST AS host, 
        PROCESSLIST_DB AS db, 
        PROCESSLIST_COMMAND AS command, 
        PROCESSLIST_TIME AS time, 
        PROCESSLIST_STATE AS state, 
        LEFT(PROCESSLIST_INFO, 80) AS info
 FROM performance_schema.threads
 WHERE PROCESSLIST_ID IS NOT NULL
 AND PROCESSLIST_COMMAND NOT IN ('Sleep', 'Binlog Dump')
 ORDER BY PROCESSLIST_TIME ASC;

But I would descend and limit by 10. The longest running query is probably the issue.
NOTE: This is similar to "show processlist". You can modify it. 

SELECT PROCESSLIST_ID AS id, 
        PROCESSLIST_USER AS user, 
        PROCESSLIST_HOST AS host, 
        PROCESSLIST_DB AS db, 
        PROCESSLIST_COMMAND AS command, 
        PROCESSLIST_TIME AS time, 
        PROCESSLIST_STATE AS state, 
        LEFT(PROCESSLIST_INFO, 80) AS info
 FROM performance_schema.threads
 WHERE PROCESSLIST_ID IS NOT NULL
 AND PROCESSLIST_COMMAND NOT IN ('Sleep', 'Binlog Dump')
 ORDER BY PROCESSLIST_TIME DESC limit 10;

-- -----------------------------------------------------------------
Here are the things we can examine
mysql> desc events_statements_history;
+-------------------------+------------------------------------------------+------+-----+---------+-------+
| Field                   | Type                                           | Null | Key | Default | Extra |
+-------------------------+------------------------------------------------+------+-----+---------+-------+
| THREAD_ID               | bigint unsigned                                | NO   | PRI | NULL    |       |
| EVENT_ID                | bigint unsigned                                | NO   | PRI | NULL    |       |
| END_EVENT_ID            | bigint unsigned                                | YES  |     | NULL    |       |
| EVENT_NAME              | varchar(128)                                   | NO   |     | NULL    |       |
| SOURCE                  | varchar(64)                                    | YES  |     | NULL    |       |
| TIMER_START             | bigint unsigned                                | YES  |     | NULL    |       |
| TIMER_END               | bigint unsigned                                | YES  |     | NULL    |       |
| TIMER_WAIT              | bigint unsigned                                | YES  |     | NULL    |       |
| LOCK_TIME               | bigint unsigned                                | NO   |     | NULL    |       |
| SQL_TEXT                | longtext                                       | YES  |     | NULL    |       |
| DIGEST                  | varchar(64)                                    | YES  |     | NULL    |       |
| DIGEST_TEXT             | longtext                                       | YES  |     | NULL    |       |
| CURRENT_SCHEMA          | varchar(64)                                    | YES  |     | NULL    |       |
| OBJECT_TYPE             | varchar(64)                                    | YES  |     | NULL    |       |
| OBJECT_SCHEMA           | varchar(64)                                    | YES  |     | NULL    |       |
| OBJECT_NAME             | varchar(64)                                    | YES  |     | NULL    |       |
| OBJECT_INSTANCE_BEGIN   | bigint unsigned                                | YES  |     | NULL    |       |
| MYSQL_ERRNO             | int                                            | YES  |     | NULL    |       |
| RETURNED_SQLSTATE       | varchar(5)                                     | YES  |     | NULL    |       |
| MESSAGE_TEXT            | varchar(128)                                   | YES  |     | NULL    |       |
| ERRORS                  | bigint unsigned                                | NO   |     | NULL    |       |
| WARNINGS                | bigint unsigned                                | NO   |     | NULL    |       |
| ROWS_AFFECTED           | bigint unsigned                                | NO   |     | NULL    |       |
| ROWS_SENT               | bigint unsigned                                | NO   |     | NULL    |       |
| ROWS_EXAMINED           | bigint unsigned                                | NO   |     | NULL    |       |
| CREATED_TMP_DISK_TABLES | bigint unsigned                                | NO   |     | NULL    |       |
| CREATED_TMP_TABLES      | bigint unsigned                                | NO   |     | NULL    |       |
| SELECT_FULL_JOIN        | bigint unsigned                                | NO   |     | NULL    |       |
| SELECT_FULL_RANGE_JOIN  | bigint unsigned                                | NO   |     | NULL    |       |
| SELECT_RANGE            | bigint unsigned                                | NO   |     | NULL    |       |
| SELECT_RANGE_CHECK      | bigint unsigned                                | NO   |     | NULL    |       |
| SELECT_SCAN             | bigint unsigned                                | NO   |     | NULL    |       |
| SORT_MERGE_PASSES       | bigint unsigned                                | NO   |     | NULL    |       |
| SORT_RANGE              | bigint unsigned                                | NO   |     | NULL    |       |
| SORT_ROWS               | bigint unsigned                                | NO   |     | NULL    |       |
| SORT_SCAN               | bigint unsigned                                | NO   |     | NULL    |       |
| NO_INDEX_USED           | bigint unsigned                                | NO   |     | NULL    |       |
| NO_GOOD_INDEX_USED      | bigint unsigned                                | NO   |     | NULL    |       |
| NESTING_EVENT_ID        | bigint unsigned                                | YES  |     | NULL    |       |
| NESTING_EVENT_TYPE      | enum('TRANSACTION','STATEMENT','STAGE','WAIT') | YES  |     | NULL    |       |
| NESTING_EVENT_LEVEL     | int                                            | YES  |     | NULL    |       |
| STATEMENT_ID            | bigint unsigned                                | YES  |     | NULL    |       |
| CPU_TIME                | bigint unsigned                                | NO   |     | NULL    |       |
| MAX_CONTROLLED_MEMORY   | bigint unsigned                                | NO   |     | NULL    |       |
| MAX_TOTAL_MEMORY        | bigint unsigned                                | NO   |     | NULL    |       |
| EXECUTION_ENGINE        | enum('PRIMARY','SECONDARY')                    | YES  |     | NULL    |       |
+-------------------------+------------------------------------------------+------+-----+---------+-------+


-------------------------
To see all queries

select thread_id, event_id, sql_text from events_statements_history  where sql_text is not NULL;

To see which queries are the worst performing in terms of rows_sent versus rows_examined.

----------------------
These are my queries.

To see worst performing queries

select   rows_examined, rows_sent, cast((rows_sent/rows_examined)*100 as unsigned)  as rows_percent, sql_text
  from events_statements_history
  where sql_text is not NULL and rows_examined > 100
  order by rows_percent ASC, rows_examined;

-----------------------------------
Queries with most rows examined

select   rows_examined, sql_text
  from events_statements_history
  where sql_text is not NULL and rows_examined > 100
  order by  rows_examined desc;

NOTE: You may want to pattern match this. 

-----------------------------------
Queries with most rows sent

select   rows_examined, sql_text
  from events_statements_history
  where sql_text is not NULL and rows_examined > 100
  order by  rows_examined desc;

NOTE: You may want to pattern match this. 

------

To get the queries with most rows examined (the busiest)
1. regex all queries and group them
2. For each query pattern, add up the rows_examined, and rows_sent.
3. Display results. 

-------------------------

Eanble all recordings, this might slow the server.
UPDATE  performance_schema.setup_instruments SET ENABLED = 'YES', TIMED = 'YES';
UPDATE performance_schema.setup_consumers SET ENABLED = 'YES';

UPDATE performance_schema.setup_instruments
SET ENABLED = 'YES', TIMED = 'YES'
WHERE NAME LIKE 'stage/%';
UPDATE performance_schema.setup_consumers
SET ENABLED = 'YES'
WHERE NAME LIKE 'events_stages%';

Get all timings for queries where statement is not null and more than 100 rows. 

select esh1.thread_id, esh2.nesting_event_id, esh2.event_id, esh2.timer_wait, esh2.event_name
       from performance_schema.events_statements_history_long esh1
       	    join performance_schema.events_stages_history_long esh2
	      on (esh1.thread_id=esh2.thread_id and esh1.event_id = esh2.nesting_event_id)
where esh1.sql_text is not NULL and esh1.rows_examined > 100;


Sum the times, display the highest.

select esh1.thread_id, esh1.event_id, sum(esh2.timer_wait)/1000000000000 as total_time, esh1.sql_text
       from performance_schema.events_statements_history_long esh1
            join performance_schema.events_stages_history_long esh2
              on (esh1.thread_id=esh2.thread_id and esh1.event_id = esh2.nesting_event_id)
       where esh1.sql_text is not NULL and esh1.rows_examined > 100
       	 and esh1.current_schema not in ('mysql', 'performance_schema')
       group by esh1.thread_id, esh1.event_id, esh1.sql_text
       order by total_time desc\G

I tried events_stages_current and events_stages_history, but they emptied the queries. Current is only if it is currently running.
Not sure about events_stages_history;

Detect highest times per stage for the highest 4 queries for stages more than 0.0001

select esh1.thread_id, esh1.event_id, sum(esh2.timer_wait)/1000000000000 as total_time, esh1.sql_text
       from performance_schema.events_statements_history_long esh1
            join performance_schema.events_stages_history_long esh2 on
	       (esh1.thread_id=esh2.thread_id and esh1.event_id = esh2.nesting_event_id)
       where esh1.sql_text is not NULL and esh1.rows_examined > 100
         and esh1.current_schema not in	('mysql', 'performance_schema')
         and esh1.sql_text not like '%performance_schema%'
       group by esh1.thread_id, esh1.event_id, esh1.sql_text
       order by total_time desc   limit 4;

Only select select statements.

create database if not exists temp;
use temp;
drop table if exists total_time;
select i3.i, i5.i2 from mark.i as i3 join mark.i2 as i5 on (i3.i = i5.i2) limit 200;

create temporary table total_time
select esh1.thread_id, esh1.event_id, sum(esh2.timer_wait)/1000000000 as total_time_ms, esh1.sql_text
       from performance_schema.events_statements_history_long esh1
            join performance_schema.events_stages_history_long esh2 on
               (esh1.thread_id=esh2.thread_id and esh1.event_id = esh2.nesting_event_id)
       where esh1.sql_text is not NULL and esh1.rows_examined > 100
      	 and esh1.current_schema not in ('mysql', 'performance_schema')
      	 and esh1.sql_text not like '%performance_schema%' and esh1.sql_text  like '%select%'
       group by esh1.thread_id, esh1.event_id, esh1.sql_text
       order by total_time_ms desc   limit 4;


Without the query.

select t.thread_id,t.event_id, esh2.nesting_event_id, esh2.event_name,
   esh2.timer_wait/1000000000 as timer_wait_ms, t.total_time_ms
       from total_time t
            join performance_schema.events_stages_history_long esh2 on
	       (t.thread_id=esh2.thread_id and t.event_id = esh2.nesting_event_id)
;


With query -- kinda of messy.

select t.thread_id,t.event_id, esh2.nesting_event_id, esh2.event_name,
    esh2.timer_wait/1000000000 as timer_wait_ms, t.total_time_ms, t.sql_text as sql1
       from total_time t
            join performance_schema.events_stages_history_long esh2 on
               (t.thread_id=esh2.thread_id and t.event_id = esh2.nesting_event_id)
;


Change format;

select t.thread_id,t.event_id, esh2.nesting_event_id, esh2.event_name,
   esh2.timer_wait/1000000000 as timer_wait_ms, t.total_time_ms, t.sql_text as sql1
       from total_time t
            join performance_schema.events_stages_history_long esh2 on
               (t.thread_id=esh2.thread_id and t.event_id = esh2.nesting_event_id)
\G

 
----------------------
TODO: Queries by otehr things, like IO